I will print this message and tape it on the blastatlas groupleader's screen. Let me know if you haven't heard from them within a week,
cheers /T -- Sicheritz-Ponten Thomas, Associate Professor, Ph.D Head of Metagenomics, Technical University of Denmark Center for Biological Sequence Analysis, BioCentrum CBS: +45 45 252422 Building 208, DK-2800 Lyngby Fax: +45 45 931585 http://www.cbs.dtu.dk/~thomas ----- Reply message ----- From: "Dan Bolser" <[email protected]> Date: Fri, Aug 26, 2011 00:04 Subject: [BiO BB] append schema to proxy To: "General Forum at Bioinformatics.Org" <[email protected]> On 25 August 2011 15:51, galeb abu-ali <[email protected]> wrote: > Hi, > > I'm trying to run a program that generates a circular genome homology atlas > "BLASTatlas" ( http://www.cbs.dtu.dk/ws/ws.php?entry=BLASTatlas ). I think > the problem is with the module that appends schemas to the proxy, and I > don't know how to do that manually. I've emailed the author couple times and > have not heard back. Pasted below is the error message. At your convenience, > I'd greatly appreciate your help. > > thanks > > galeb > > p/s - also, is there another program that can generate concetric circular > plots of BLAST scores for multiple bacterial genomes with a per nucleotide > resolution? thanks Since this looks like a Perl program, I've CC'ed this reply to the BioPerl mailing list in case anyone there can provide specific help. If I understood what you want to do, you could try Circos [1]. Why don't you keep the author of BLASTatlas CC'ed in these mails? Cheers, Dan. [1] http://circos.ca/ > [galeb@localhost GeneWiz]$ BLASTatlas -modus circle -ref BX571966.fsa > -proteins BX571966.proteins.fsa -ann BX571966.ann -blastcfg blast.cfg > -customcfg custom.cfg --dnap="Intrinsic Curvature,Stacking Energy,Position > Preference" -title "B. pseudomallei K96243" > sgeneric.ps > # title set to 'B. pseudomallei K96243' > # output format is ps > # modus is 'circle' > # loading reference genome ... > # loading proteins ... > # parsing blast lane configuration (blast.cfg) ... > # .. parsing blast lane (B. ubonensis Bu) ... > # .. .. program: tblastn > # .. .. parsing color 101010_040410 > # .. .. .. color from: r:10, g:10, b:10 > # .. .. .. color to: r:04, g:04, b:10 > # .. .. byrange: 0 .. 0.8 > # .. parsing sequene source 'cat ./19539.fsa |' ... 1142 done > # .. parsing blast lane (B. pseudomallei DM98) ... > # .. .. program: tblastn > # .. .. parsing color 101010_040410 > # .. .. .. color from: r:10, g:10, b:10 > # .. .. .. color to: r:04, g:04, b:10 > # .. .. byrange: 0 .. 0.8 > # .. parsing sequene source 'cat ./19509.fsa |' ... 2370 done > # parsing custom lane configuration (custom.cfg) ... > # .. parsing custom data entry [email protected] ... > # .. .. parsing color 000010_101010 > # .. .. .. color from: r:00, g:00, b:10 > # .. .. .. color to: r:10, g:10, b:10 > # .. .. byrange: 9 .. 10 > # .. .. boxfilter 5000 ... > # .. parsing data source 'gunzip -c BX571966- > 57a2f2c2e11ca0dd8cd74493d667d4d6-3173005.sidd--0.035-c-10-c.out.gz | cut -f4 > |' ... > # .. .. parsing data source ... 3173005 done > # reading external files and build hash of sequences ... > *panic: schemas() removed in v2.00, not needed anymore* > at /usr/local/lib/perl5/site_perl/5.12.2/XML/Compile/WSDL11.pm line 65 > XML::Compile::WSDL11::schemas(XML::Compile::WSDL11=HASH(0x1fed6740)) at > xml-compile.pl line 48 > main::appendSchemas(XML::Compile::WSDL11=HASH(0x1fed6740), " > http://www.cbs.dtu.dk/ws/common/ws_common_1_0b.xsd";, " > http://www.cbs.dtu.dk/ws/BLASTatlas/ws_blastatlas_1_0_ws2.xsd";) at > BLASTatlas line 177appen > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
